def test_types_ffld(self):
qstruct = QStruct("data/ace_ash_nma.pdb", "pdb")
qprm = QPrm("oplsaa")
qprm.read_ffld("data/ace_ash_nma.ffld11", qstruct)
print(list(qprm.torsions.keys()))
lj_A_i = (4 * 0.17 * ((3.25)**12))**0.5
lj_B_i = (4 * 0.17 * ((3.25)**6))**0.5
at = qprm.atom_types["nma.N"]
assert is_close(at.lj_A, lj_A_i)
assert is_close(at.lj_B, lj_B_i)
bond = qprm.bonds["ace.C ace.CH3"]
assert is_close(bond.fc / 2.0, 317.0)
assert is_close(bond.r0, 1.522)
ang = qprm.angles["ash.C ash.CA ash.CB"]
assert is_close(ang.fc / 2.0, 63.0)
assert is_close(ang.theta0, 111.1)
tors = qprm.torsions["ace.C ash.N ash.CA ash.C"]
assert is_close(tors.fcs[0] * 2.0, -2.365)
assert is_close(tors.fcs[1] * 2.0, 0.912)
assert is_close(tors.fcs[2] * 2.0, -0.850)
assert is_close(tors.multiplicities[0], 1.0)
assert is_close(tors.multiplicities[1], 2.0)
assert is_close(tors.multiplicities[2], 3.0)
assert is_close(tors.phases[0], 0.0)
assert is_close(tors.phases[1], 180.0)
assert is_close(tors.phases[2], 0.0)
def test_wrong_ff_fail(self):
qprm = QPrm("amber")
with pytest.raises(QPrmError):
qprm.read_ffld("data/ace_ash_nma.ffld11", None)
qprm = QPrm("oplsaa")
with pytest.raises(QPrmError):
qprm.read_amber_parm("data/ff-amber14/parm/parm10.dat")
with pytest.raises(QPrmError):
qprm.read_amber_frcmod("data/ff-amber14/parm/frcmod.ff14SB")
def test_read_ffld(self):
qstruct = QStruct("data/ace_ash_nma.pdb", "pdb")
qprm = QPrm("oplsaa")
qprm.read_ffld("data/ace_ash_nma.ffld11", qstruct)
assert len(qprm.atom_types) == 25
assert len(qprm.bonds) == 24
assert len(qprm.angles) == 40
assert len(qprm.torsions) == 49
assert len(qprm.impropers) == 5
#
# create QLib, QPrm, QStruct and QTopology objects
#
qlib = QLib("oplsaa", ignore_errors=args.ignore_errors)
qprm = QPrm("oplsaa", ignore_errors=args.ignore_errors)
try:
qstruct = QStruct(args.pdb, "pdb", ignore_errors=args.ignore_errors)
except QStructError as err:
print "FATAL! Problem with pdb: {}".format(err)
sys.exit(1)
try:
qprm.read_ffld(args.ffld_output, qstruct)
except QPrmError as err:
print "FATAL! Problem with ffld file: {}".format(err)
sys.exit(1)
try:
qlib.read_ffld(args.ffld_output, qstruct)
except QLibError as err:
print "FATAL! Problem with ffld file: {}".format(err)
sys.exit(1)
try:
qtop = QTopology(qlib, qprm, qstruct)
except QTopologyError as err:
print "FATAL! Problem building the topology: {}".format(err)
